Word count is found in the right-hand navigation menu.
The bar chart seen on the right is your project word count (or can include all projects if you click to toggle it).
If you are using goals, you can choose a Book, the Manuscript, or the entire Project as your target. Word count in the status bar and at the top of the book is inclusive of all words within the selected document and none from outside it.
1. Words from Story Notes won’t be counted in goals unless you choose “Project."
2. When you click on the Book you get the word count for the book only, nothing that has been removed from it (which could explain negative word count for the day’s count).